Artedi accidentally drowned at Amsterdam, where he was engaged in cataloguing the collections of Albertus Seba, a wealthy Dutchman, who had formed what was perhaps the richest museum of his time. According to agreement, his manuscripts came into the hands of Linnaeus, and his Bibliotheca Ichthyologica and Philosophia Ichthyologica, together with a life of the author, were published at Leiden in 1738 under the title "Ichthyologia sive opera omnia de piscibus ..." .

Artedi was buried in a pauper's grave in St Anthony's churchyard in Amsterdam on 2 October 1735. His grave was never marked and the churchyard site has since been appropriated for other purposes. An epitaph, written in Latin by Anders Celsius, and translated into English by George Shaw, is known because it was inscribed on the back flyleaf of Linnaeus's own copy of "Ichthyologia":

Here lies poor Artedi, in foreign land pyx'd

Not a man nor a fish, but something betwixt,

Not a man, for his life among fishes he past,

Not a fish, for he perished by water at last.

A memorial stone to Peter Artedi was erected in Amsterdam Zoological Gardens and unveiled on 28 June 1905; it is inscribed in Latin. Other stone memorials are in Anundsjö and Nordmaling in Sweden.

Linnaeus named Artedia[1] (Apiaceae), a monotypic genus from the eastern Mediterranean, after his friend.